by Liz Szabo, USA TODAY

by Liz Szabo, USA TODAY

Scientists are searching for clues to the resurgence of whooping cough, a nearly forgotten childhood infection causing outbreaks around the country.

California last week announced a whooping cough epidemic, reporting more than 800 cases in two weeks, along with two deaths in infants. Nationwide, the Centers for Disease Control and Prevention reports nearly 10,000 cases so far this year of whooping cough, also known as pertussis.

Although whooping cough is cyclical, peaking every three to five years, cases have soared in the past decade, with 48,277 cases in 2012, the largest number in 50 years.

The best defense against whooping cough is vaccination, says Ron Chapman, director of the California Department of Public Health.

Research shows that unvaccinated children are eight times more likely to contract whooping cough than those children who get vaccines. The CDC recommends vaccines for both children and adults, including everyone likely to come in contact with newborns. Pregnant women should get a whooping cough shot with each pregnancy, in order to protect babies in the first months of life.

Parents who skip vaccinations for their children have driven outbreaks of measles across the United States, according to the CDC.

But vaccine refusal appears to be playing a much smaller role in whooping cough epidemics, says William Schaffner, a professor at the Vanderbilt University School of Medicine.

Instead, studies show that the vaccine against whooping cough may not be protective enough, Schaffner says. Studies show that the current whooping cough vaccine - called DTaP, used since the 1990s - only provides strong protection for the first few years. Protection appears to wane after that, leaving kids vulnerable to infection after four to six years.

That could explain why whooping cough rates began rising in the early 2000s. An earlier version of the whooping cough vaccine - called DTP - provided more long-lasting protection. That vaccine was phased out, however, due to concerns that it caused bothersome reactions in babies, such as irritability and long bouts of crying, Schaffner says. Although the vaccine was never conclusively linked to serious side effects, concerns over its safety helped propel the modern anti-vaccine movement, which has led many of today's parents to skip or space out their children's shots, Schaffner says.

The vaccine could have other limitations, as well.

A study published by the Food and Drug Administration in November found that whooping cough vaccines kept animals from becoming sick, but allowed them to serve as silent carriers of the illness, able to infect others. Although the study was conducted in baboons, scientists say its findings likely apply to humans, as well, Schaffner says.

Lastly, the bacteria that causes whooping cough appears to be mutating in ways that make it less susceptible to the current vaccine, says CDC scientist Lucia Pawloski. Doctors first noticed genetic mutations in a key protein used to make the vaccine, called pertactin, in 1994. Those changes weren't found again until 2000.

Recent tests, however, have found the mutations in 60% of whooping cough samples, Pawloski says.

Although scientists are concerned about the mutations, there's no sign yet that those mutations are driving the outbreaks.

These findings underscore the need for scientists to develop a better whooping cough vaccine, Schaffner says.

Pawloski notes that whooping cough is different from other infectious diseases, which may help explain why it's been so hard to eradicate.

While people infected with chickenpox or measles typically get lifelong protection from the illness, even those infected "naturally" with whooping cough don't get lifelong immunity, Schaffner says. Studies show that people who contract whooping cough can get the disease again a decade later.